I rode in Mobile bay last week. Water temps is in the upper 50's, lower 60's. I have the 787cc powered GTX. Though, it is prudent to make sure your motor is warm, you do have a pre-heater (your exhaust) that warms your water that cools your jugs, before entering the block. Warm it up a little, then have a great time. The cooling system is set up with calibrated fittings, that works like a thermostat in a way, by allowing the water to flow at a restricted rate. The water has time to warm up before leaving the motor.
If you think about the guys up north, running their sleds in the snow, in temps under 30*F, they have no temperature related problems. These older models use the Rotax 2 stroke (Ski-Doo) motor, though it's air-cooled, not water.
Because cold air is dense, heavier than warm air, you might find the need to use your choke at half open till the motor is warm enough to run on it's own. THen again, you might not. Last week, I had to run my choke half way our for about one minute, till the motor started to heat up. Go out and have fun, get some time on your new rebuild. Make sure you use more oil for the break-in. Now is more important than summer, because of the air flow.